CN by cancer type

The plot below looks at relative log2 CN across the different lineages. The dashed lines mark the cutoffs for deep (< -0.7), shallow (-0.7 < CN < -0.2), and neutral (-0.2 < CN < 0.2) cutoffs.

The table below outlines the numbers for types of CN events for VPS4A and VPS4B in the TCGA data.

The plot below is the same as above but this time using absolute CN (relative CN * ploidy from ABSOLUTE)

Combined VPS4A+B CN score

In the plot below, for each sample, we are calculating a combined VPS4A/B CN score (sum of the two relative CN), and then plotting by lineage. In this plot, because we are looking at CN of VPS4A + VPS4B and then taking the log2, we expect that ‘normal’ is around 1 (as 2^1=2).

Combined VPS4A/B expression/CN with dependency data

Given how related VPS4A/B are, we are interested in seeing if combining the expression/CN of these two genes to generate one VPS4 expression/CN score is more strongly associated with VPS4A/B dependency and if potentially other interested targets fall out in dependency space.

Expression

To start and to keep things simple, we will create a total VPS4 expression score by summing the expression of VPS4A/B in depmap data. We will call this new score VPS4A_B in the plots below.

CN

To start and to keep things simple, we will create a total VPS4 expression score by summing the expression of VPS4A/B in depmap data. We will call this new score VPS4A_B in the plots below

RNA and CN correlation in TCGA

We generated a similar plots in CCLE. We are interested to see where the relationship between VPS4A/B expression and copy number falls in relation to other genes in TCGA. In the plots below, we plot the correlation of expression and relative copy number of a set of 4000 randomly selected genes and VPS4A and VPS4B. There are also individual plots for VPS4A/B expression and CN in the cohort.